Related papers: Mod/Resc Parsimony Inference
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
Bayesian inference for exponential family random graph models (ERGMs) is a doubly-intractable problem because of the intractability of both the likelihood and posterior normalizing factor. Auxiliary variable based Markov Chain Monte Carlo…
Gene-gene interactions are often regarded as playing significant roles in influencing variabilities of complex traits. Although much research has been devoted to this area, to date a comprehensive statistical model that addresses the…
We introduce a method to identify heritable microbiome communities when the input is a pairwise dissimilarity matrix among all samples. Current methods target each taxon individually and are unable to take advantage of their phylogenetic…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Probabilistic Boolean Networks play a remarkable role in the modelling and control of gene regulatory networks. In this paper, we consider the inverse problem of constructing a sparse probabilistic Boolean network from the prescribed…
Bootstrap percolation is a process that is used to model the spread of an infection on a given graph. In the model considered here each vertex is equipped with an individual threshold. As soon as the number of infected neighbors exceeds…
This paper addresses the problem of identifying parsimonious explicit piece-wise polynomial relationships that might involve a relatively large number of raw features. The algorithm leverages a recently proposed identification algorithm…
We study the problem of experimental design for accurately identifying the causal graph structure of a simple structural causal model (SCM), where the underlying graph may include both cycles and bidirected edges induced by latent…
Bacterial cellulose is an important class of biomaterials which can be grown in well-controlled laboratory and industrial conditions. The cellulose structure is affected by several biological, chemical and environmental factors, including…
Theoretical studies on evolutionary algorithms have developed vigorously in recent years. Many such algorithms have theoretical guarantees in both running time and approximation ratio. Some approximation mechanism seems to be inherently…
In this paper, we investigate the butterfly factorization problem, i.e., the problem of approximating a matrix by a product of sparse and structured factors. We propose a new formal mathematical description of such factors, that encompasses…
Covering and elimination inequalities are central to combinatorial optimization, yet their role has largely been studied in problem-specific settings or via no-good cuts. This paper introduces a unified perspective that treats these…
Cell injection is a technique in the domain of biological cell micro-manipulation for the delivery of small volumes of samples into the suspended or adherent cells. It has been widely applied in various areas, such as gene injection,…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
In this paper we present recent results on parametric analysis of biological models. The underlying method is based on the algorithms for computing trajectory sets of hybrid systems with polynomial dynamics. The method is then applied to…
The study of control mechanisms of biological systems allows for interesting applications in bioengineering and medicine, for instance in cell reprogramming or drug target identification. A control strategy often consists of a set of…
A common task in experimental sciences is to fit mathematical models to real-world measurements to improve understanding of natural phenomenon (reverse-engineering or inverse modeling). When complex dynamical systems are considered, such as…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Insects like dragonflies and cicadas possess nanoprotusions on their wings that rupture bacterial membranes upon contact, inspiring synthetic antibacterial surfaces mimicking this phenomenon. Designing such biomimetic surfaces requires…